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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411
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        Tool Citations

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        About MultiQC

        This report was generated using MultiQC, version 1.29

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2025-05-29, 09:07 IDT based on data in: /lustre1/home/mass/amalia/montipora_mapping/outputs/stringtie

        General Statistics

        Showing 9/9 rows and 1/2 columns.
        Sample NameAssignedAssigned
        SRR14864064
        28.0M
        28.1%
        SRR14864065
        22.5M
        25.0%
        SRR14864066
        17.4M
        19.2%
        SRR14864067
        38.7M
        50.2%
        SRR14864068
        32.4M
        49.6%
        SRR14864069
        37.8M
        55.3%
        SRR14864070
        38.5M
        55.9%
        SRR14864071
        39.9M
        48.6%
        SRR14864072
        34.1M
        49.8%

        GffCompare

        Version: 0.12.9

        Tool to compare, merge and annotate one or more GFF files with a reference annotation in GFF format.URL: https://ccb.jhu.edu/software/stringtie/gffcompare.shtmlDOI: 10.12688/f1000research.23297.1

        Accuracy values

        Displayed are the accuracy values precisiond and sensitivity for different levels of genomic features. The metrics are calculated for the comparison of a query and reference GTF file.

        Accuracy metrics are calculated as described in Burset et al. (1996). Sensitivity is the true positive rate, Precision True Positives are query features that agree with features in the reference. The exact definition depends on the feature level:

        • Base: True positives are bases reported at the same coordinates.
        • Exon: Comparison units are exons that overlap in query and reference with same coordinates.
        • Intron chain: True positives are query transcripts for which all introns coordinates match those in the reference.
        • Transcript: More stringent then intron chain, all Exon coordinates need to match. Outer exon coordinates (start + end) can vary by 100 bases in default settings
        • Locus: Cluster of exons need to match.

        A more in depth description can be found here.

        Created with MultiQC

        Novel features

        Number of novel features, present in the query data but not found in the reference annotation.

        Created with MultiQC

        Missing features

        False negative features, which are found in the reference annotation but missed (not present) in the query data.

        Created with MultiQC

        featureCounts

        Counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.URL: http://subread.sourceforge.netDOI: 10.1093/bioinformatics/btt656

        Assignments

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        GffCompare0.12.9

        MultiQC v1.29 - Written by Phil Ewels, available on GitHub.

        This report uses Plotly, jQuery, jQuery UI, Bootstrap and FileSaver.js.